Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes

Abstract

BackgroundStreptococcus agalactiae, also known as Group B Streptococcus (GBS), is a Gram-positive bacterium that colonizes the gastrointestinal and genitourinary tract of humans. This bacterium has also been isolated from various animals, such as fish and cattle. Non-coding RNAs (ncRNAs) can act as regulators of gene expression in bacteria, such as Streptococcus pneumoniae and Streptococcus pyogenes. However, little is known about the genomic distribution of ncRNAs and RNA families in S. agalactiae.ResultsComparative genome analysis of 27 S. agalactiae strains showed more than 5 thousand genomic regions identified and classified as Core, Exclusive, and Shared genome sequences. We identified 27 to 89 RNA families per genome distributed over these regions, from these, 25 were in Core regions while Shared and Exclusive regions showed variations amongst strains. We propose that the amount and type of ncRNA present in each genome can provide a pattern to contribute in the identification of the clonal types.ConclusionsThe identification of RNA families provides an insight over ncRNAs, sRNAs and ribozymes function, that can be further explored as targets for antibiotic development or studied in gene regulation of cellular processes. RNA families could be considered as markers to determine infection capabilities of different strains. Lastly, pan-genome analysis of GBS including the full range of functional transcripts provides a broader approach in the understanding of this pathogen.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4951-z) contains supplementary material, which is available to authorized users.

Comparative Genomics of Degradative Novosphingobium Strains With Special Reference to Microcystin-Degrading Novosphingobium sp. THN1

“…The percentage of distributed genes in the each genome varied from 76.43 to 86.36%. Similarly, the alignments of 27 Streptococcus agalactiae genomes revealed a great number of distributed genes (72.15%) (Wolf et al, 2018 ). However, the comparative analyses revealed a relative low proportion of distributed genes in 24 Shewanella strains (42.7%), five drug-resistance Aeromonas hydrophila strains (14.02–32.75%), 23 Pasteurella multocida strains (33.47%) and Microcystis aeruginosa strains (38–48%) (Humbert et al, 2013 ; Hurtado et al, 2018 ; Zhang et al, 2018 ; Zhong et al, 2018 ).…”

Genomic Insights into the Diversity of Non-Coding RNAs in Bacillus Cereus Sensu Lato.

“…This class of ncRNAs consists of elements characterized as ribozymes that act as mobile genetic elements (Harris and Breaker 2018;Toro et al 2018;Fayad et al 2019). Therefore, the abundance of these elements in B. cereus group strains reinforces the role of horizontal genetic transfer (HGT) in genome plasticity, evolution, and the acquisition of novel ncRNAs, as already observed for Streptococcus agalactiae (Wolf et al 2018).…”

“…However, the results of the comparative analysis of ncRNAs in other bacterial groups highlight the importance of these genetic elements for the adaptation of bacteria to the environment. Thus, Wolf (2018), in a previous work developed by our research group, veri ed a great variation of ncRNAs in S. agalactiae strains, which were distributed in three clusters, corresponding to different hosts (Cluster 0: sh; Cluster 1: mammals; and Cluster 2: sh and mammals). In addition, they observed a correlation between the number of RNA families and the origin (cluster) of the strains, demonstrating that ncRNAs may be involved with the bacterial-host interaction in pathogenic species.…”

Global Annotation, Expression Analysis, and Stability of Candidate sRNAs in Group B Streptococcus

“…Pichon et al utilized in silico analysis to identify 197 novel sRNA candidates ( 8 ), and subsequent work by Rosinski-Chupin et al utilized differential RNA sequencing (dRNA-seq) and strand-specific RNA sequencing (RNA-seq) to identify 120 putative sRNAs ( 9 ). These sRNAs were later classified by Wolf et al into conserved RNA families across 27 GBS genomes ( 10 ). However, because only those with high structural similarity to known bacterial sRNAs were analyzed, only 30 GBS sRNAs were classified in this study, potentially excluding many legitimate GBS sRNAs.…”